rs624704

chr9-21383899-A-Gchr9-21383899-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000698342.1(MIR31HG):n.726-3540T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,956 control chromosomes in the GnomAD database, including 16,934 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (16934 hom., cov: 32)
• Consequence: MIR31HG ENST00000698342.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.93

Genes affected

MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIR31HG	ENST00000698342.1	n.726-3540T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65777 AN: 151840 Hom.: 16907 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.383

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.433 AC: 65863 AN: 151956 Hom.: 16934 Cov.: 32 AF XY: 0.434 AC XY: 32259 AN XY: 74288

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.385

Alfa AF: 0.404 Hom.: 2622

Bravo AF: 0.454

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.028
Dann	Benign	0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs624704; hg19: chr9-21383898;